Rduckhts - 'DuckDB' High Throughput Sequencing File Formats Reader Extension
Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API <https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
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bamduckdb-extensionfastqhtslibvcf
5.37 score 15 stars 13 scripts 377 downloadsRBCFTools - 'BCFTools', 'libbcftools' and 'htslib' Wrappers and 'BCF'/'VCF' to 'Parquet' Convertors
Bundles the 'htslib' and 'bcftools' libraries and command lines tools for reading and manipulating VCF/BCF files. Includes streaming facilities from VCF to Apache Arrow via 'nanoarrow', enabling export to Arrow IPC format and Parquet format using 'duckdb' including a 'bcf_reader' extension. Utilities for reading and writing VCF/BCF files into 'DuckLake' are included. provided.
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bcftoolsduckdbducklakegenomicshtslibnanoarrowparquet
3.19 score 2 stars 22 scripts